pyrenew-flu-light

⚠️ This is a work in progress.

pyrenew-flu-light is an influenza forecasting model (originally written in R, using the package Epidemia, with the name cfaepim) that has been re-instantiated via PyRenew.

NOTE: Presently, this pyrenew-flu-light cannot be installed and used with current NHSN data.

Usage

PFL (pyrenew-flu-light) can be used in two modes: "active" and "historical". The "active" mode uses respiratory incidence data sourced from available API frameworks whereas the "historical" mode relies on saved dataset snapshots (currently, these snapshots are from the 2023-24 NHSN data, and were generated by cfaepim code).

Before running PFL, installing poetry and creating a virtual environment will very likely be necessary. This can be first done via pipx install poetry (see Poetry website for more information) and then, to create the environment, poetry install followed by poetry shell in the PFL folder (only done after cloning: git clone https://github.com/CDCgov/pyrenew-flu-light).

After poetry shell has been run, then to use the "historical" mode (once within the folder pyrenew_flu_light), the run.py file creates an experiment. Each experiment generates forecasts based on selected jurisdictions and a configuration file. The configuration files for the "historical" mode are derived from the configuration files used in cfaepim; the reader will most often never need to worry about configuration files in the "historical" mode. To run:

``` poetry run python run.py --reportingdate 2024-01-20 --regions NY,AL,CA --historical --forecast --expname experiment_01

poetry run python run.py --reportingdate 2024-03-30 --regions not:NY,AL,CA --historical --forecast --expname experiment_02 ```

...Contained Within This Repository

• [ ] A pull request template
• [ ] A website.
• [x] An Apache 2.0 license
• [x] An issue template (taken from PyRenew).
• [x] A pre-commit schema.
• [x] A .gitignore file (taken from PyRenew).
• [x] Formal contribution language (hybrid, from cdcent)

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